Why I am seeing patches of diffirent transparency in this model with GLSL
Answering here as well for completeness sake.

The issue with occlusion is fixed in blender, but the issue with sections having more or less transparency is not

The cause is that faces of transparent objects in blender are drawn randomly. Due to depth culling, if a front face is rendered first, then all faces behind it will get culled. So randomly, some parts of the mesh will get the face closer to the view rendered first and have the most transparency, while other parts will get more than one face rendered and be more opaque.

To solve this we would need to render faces sorted from back to front, but to keep viewport performance fast in blender, we skip this currently.